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[WIP] Another shed enabled workflow test.#777

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jmchilton wants to merge 1 commit intogalaxyproject:masterfrom
jmchilton:shed_workflow_test
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[WIP] Another shed enabled workflow test.#777
jmchilton wants to merge 1 commit intogalaxyproject:masterfrom
jmchilton:shed_workflow_test

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@jmchilton jmchilton commented Feb 26, 2018

@jmchilton jmchilton force-pushed the shed_workflow_test branch 2 times, most recently from 561d704 to 90457d0 Compare March 2, 2018 00:52
@jmchilton jmchilton mentioned this pull request Mar 2, 2018
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jmchilton commented Mar 2, 2018

Added code to circumvent the dependency problems (since they weren't for tools the workflow actually used - just other tools in the repo). And now the test didn't work because it takes too long to install everything I think.

@jmchilton jmchilton force-pushed the shed_workflow_test branch from 90457d0 to f8982df Compare March 7, 2018 04:26
@jmchilton jmchilton force-pushed the shed_workflow_test branch from f8982df to 250522c Compare May 7, 2018 17:24
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jmchilton commented May 7, 2018

galaxy.tools.deps DEBUG 2018-05-07 17:55:46,530 Using dependency bcftools version 1.5 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:46,531 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-05-07 17:55:46,557 (4) command is: rm -rf working; mkdir -p working; cd working; /tmp/tmpva5iYO/job_working_directory/000/4/tool_script.sh; return_code=$?; cd '/tmp/tmpva5iYO/job_working_directory/000/4';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
export PATH=$PATH:'/home/travis/miniconda3/envs/__bcftools@1.5/bin' ; python "/tmp/tmpva5iYO/job_working_directory/000/4/set_metadata_yu5XlT.py" "/tmp/tmpva5iYO/job_working_directory/000/4/registry.xml" "/tmp/tmpva5iYO/job_working_directory/000/4/working/galaxy.json" "/tmp/tmpva5iYO/job_working_directory/000/4/metadata_in_HistoryDatasetAssociation_4_V8xGoh,/tmp/tmpva5iYO/job_working_directory/000/4/metadata_kwds_HistoryDatasetAssociation_4_k_YiQz,/tmp/tmpva5iYO/job_working_directory/000/4/metadata_out_HistoryDatasetAssociation_4__Ri3nE,/tmp/tmpva5iYO/job_working_directory/000/4/metadata_results_HistoryDatasetAssociation_4_WxtDyt,/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_4.dat,/tmp/tmpva5iYO/job_working_directory/000/4/metadata_override_HistoryDatasetAssociation_4_iQNCny" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:55:46,629 (4) executing job script: /tmp/tmpva5iYO/job_working_directory/000/4/galaxy_4.sh
galaxy.jobs DEBUG 2018-05-07 17:55:46,672 (4) Persisting job destination (destination id: upload_dest)
127.0.0.1 - - [07/May/2018:17:55:46 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:55:46,849 execution finished: /tmp/tmpva5iYO/job_working_directory/000/3/galaxy_3.sh
galaxy.model.metadata DEBUG 2018-05-07 17:55:47,031 loading metadata from file for: HistoryDatasetAssociation 3
galaxy.jobs DEBUG 2018-05-07 17:55:47,175 job 3 ended (finish() executed in (318.422 ms))
galaxy.jobs.runners.local DEBUG 2018-05-07 17:55:52,260 execution finished: /tmp/tmpva5iYO/job_working_directory/000/4/galaxy_4.sh
galaxy.model.metadata DEBUG 2018-05-07 17:55:52,397 loading metadata from file for: HistoryDatasetAssociation 4
galaxy.jobs DEBUG 2018-05-07 17:55:52,495 job 4 ended (finish() executed in (225.699 ms))
127.0.0.1 - - [07/May/2018:17:55:52 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:52 +0000] "GET /api/histories/5729865256bc2525/contents/54f2a3a23292eb07?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:52 +0000] "GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:52 +0000] "GET /api/datasets/54f2a3a23292eb07?hda_ldda=hda&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:52 +0000] "GET /api/datasets/8155e4b4bf1581ff?hda_ldda=hda&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,985 Creating a step_state for step.id 7
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,986 Creating a step_state for step.id 9
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,986 Creating a step_state for step.id 6
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,986 Creating a step_state for step.id 8
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,987 Creating a step_state for step.id 5
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,987 Creating a step_state for step.id 4
galaxy.workflow.run_request INFO 2018-05-07 17:55:52,987 Creating a step_state for step.id 3
galaxy.workflow.scheduling_manager INFO 2018-05-07 17:55:52,988 Queueing workflow invocation for handler [main]
/home/travis/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value 'copy_inputs_to_history'. (this warning may be suppressed after 10 occurrences)
(util.ellipses_string(value),))
/home/travis/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value 'meta'. (this warning may be suppressed after 10 occurrences)
(util.ellipses_string(value),))
/home/travis/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:185: SAWarning: Unicode type received non-unicode bind param value 'use_cached_job'. (this warning may be suppressed after 10 occurrences)
(util.ellipses_string(value),))
127.0.0.1 - - [07/May/2018:17:55:52 +0000] "POST /api/workflows/5729865256bc2525/invocations?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.workflow.run DEBUG 2018-05-07 17:55:53,789 Workflow step 7 of invocation 2 invoked (3.852 ms)
galaxy.workflow.run DEBUG 2018-05-07 17:55:53,792 Workflow step 9 of invocation 2 invoked (3.433 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:53,888 Handled output named outfile for tool toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 (31.822 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:53,894 Added output datasets to history (6.191 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:53,902 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] (3.984 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:53,902 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] complete, ready to flush (8.015 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:53,939 Flushed transaction for job Job[id=5,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] (35.923 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:53,939 Tool [toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] created job [5] (97.955 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:53,970 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 request: (176.839 ms)
galaxy.workflow.run DEBUG 2018-05-07 17:55:53,985 Workflow step 6 of invocation 2 invoked (192.282 ms)
127.0.0.1 - - [07/May/2018:17:55:53 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.actions INFO 2018-05-07 17:55:54,131 Handled output named out_file1 for tool toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0 (57.846 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,147 Added output datasets to history (15.401 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,174 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0] (11.900 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,176 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0] complete, ready to flush (26.507 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,244 Flushed transaction for job Job[id=6,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0] (67.520 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,245 Tool [toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0] created job [6] (224.827 ms)
127.0.0.1 - - [07/May/2018:17:55:54 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,308 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0 request: (287.654 ms)
galaxy.workflow.run DEBUG 2018-05-07 17:55:54,332 Workflow step 8 of invocation 2 invoked (346.132 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,396 Handled output named outfile for tool toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 (19.242 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,409 Added output datasets to history (13.395 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,416 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] (3.250 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,417 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] complete, ready to flush (7.042 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,438 Flushed transaction for job Job[id=7,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] (21.016 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,438 Tool [toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] created job [7] (82.399 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,457 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 request: (100.979 ms)
galaxy.workflow.run DEBUG 2018-05-07 17:55:54,464 Workflow step 5 of invocation 2 invoked (132.404 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,506 Handled output named outfile for tool toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 (16.879 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,510 Added output datasets to history (4.480 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,516 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] (3.136 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,517 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] complete, ready to flush (6.603 ms)
127.0.0.1 - - [07/May/2018:17:55:54 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.actions INFO 2018-05-07 17:55:54,567 Flushed transaction for job Job[id=8,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] (49.861 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,568 Tool [toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0] created job [8] (95.779 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,615 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 request: (142.949 ms)
galaxy.workflow.run DEBUG 2018-05-07 17:55:54,640 Workflow step 4 of invocation 2 invoked (175.269 ms)
127.0.0.1 - - [07/May/2018:17:55:54 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.actions INFO 2018-05-07 17:55:54,786 Handled output named output for tool toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1 (17.302 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,798 Added output datasets to history (12.211 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,813 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1] (6.193 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,813 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1] complete, ready to flush (15.007 ms)
galaxy.tools.actions INFO 2018-05-07 17:55:54,837 Flushed transaction for job Job[id=9,tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1] (23.088 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,837 Tool [toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1] created job [9] (149.513 ms)
galaxy.tools.execute DEBUG 2018-05-07 17:55:54,869 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1 request: (182.037 ms)
galaxy.jobs DEBUG 2018-05-07 17:55:54,872 (5) Working directory for job is: /tmp/tmpva5iYO/job_working_directory/000/5
galaxy.jobs.handler DEBUG 2018-05-07 17:55:54,880 (5) Dispatching to planemo_runner runner
galaxy.workflow.run DEBUG 2018-05-07 17:55:54,897 Workflow step 3 of invocation 2 invoked (254.223 ms)
galaxy.jobs DEBUG 2018-05-07 17:55:54,935 (5) Persisting job destination (destination id: planemo_dest)
galaxy.jobs.runners DEBUG 2018-05-07 17:55:54,941 Job [5] queued (59.051 ms)
galaxy.jobs.handler INFO 2018-05-07 17:55:54,956 (5) Job dispatched
galaxy.jobs DEBUG 2018-05-07 17:55:54,969 (6) Working directory for job is: /tmp/tmpva5iYO/job_working_directory/000/6
galaxy.jobs.handler DEBUG 2018-05-07 17:55:54,981 (6) Dispatching to planemo_runner runner
galaxy.jobs DEBUG 2018-05-07 17:55:55,027 (6) Persisting job destination (destination id: planemo_dest)
127.0.0.1 - - [07/May/2018:17:55:54 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.runners DEBUG 2018-05-07 17:55:55,051 Job [6] queued (69.287 ms)
galaxy.jobs.handler INFO 2018-05-07 17:55:55,083 (6) Job dispatched
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,449 Using dependency gawk version 4.1.3 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,458 Using dependency gawk version 4.1.3 of type conda
127.0.0.1 - - [07/May/2018:17:55:55 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.command_factory INFO 2018-05-07 17:55:55,524 Built script [/tmp/tmpva5iYO/job_working_directory/000/5/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/travis/miniconda3/envs/__gawk@4.1.3" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/travis/miniconda3/bin/activate '/home/travis/miniconda3/envs/__gawk@4.1.3' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; awk --version | head -n 1 > /tmp/tmpva5iYO/tmp/GALAXY_VERSION_STRING_5 2>&1; awk -v OFS=" " --re-interval --sandbox '{ $1 = gensub( /[0-9]+/, "chr&", "g", $1 ) ; print $0 ; }' "/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_4.dat" > "/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_5.dat"]
127.0.0.1 - - [07/May/2018:17:55:55 +0000] "GET /api/jobs?history_id=5729865256bc2525&key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,698 Using dependency bx-python version 0.7.1 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,698 Using dependency galaxy-ops version 1.0.0 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,699 Using dependency bx-python version 0.7.1 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,700 Using dependency galaxy-ops version 1.0.0 of type conda
galaxy.jobs.command_factory INFO 2018-05-07 17:55:55,833 Built script [/tmp/tmpva5iYO/job_working_directory/000/6/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/travis/miniconda3/envs/mulled-v1-a4cb0f5781d6f9de5e288400a2ac9fa34202068e5723b723249629522600dc67" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/travis/miniconda3/bin/activate '/home/travis/miniconda3/envs/mulled-v1-a4cb0f5781d6f9de5e288400a2ac9fa34202068e5723b723249629522600dc67' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/travis/miniconda3/envs/mulled-v1-a4cb0f5781d6f9de5e288400a2ac9fa34202068e5723b723249629522600dc67" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/travis/miniconda3/bin/activate '/home/travis/miniconda3/envs/mulled-v1-a4cb0f5781d6f9de5e288400a2ac9fa34202068e5723b723249629522600dc67' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; python '/home/travis/.planemo/profiles/travisworkflowtests/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/077f404ae1bb/get_flanks/get_flanks.py' '/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_3.dat' '/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_6.dat' 12000 Upstream start -o 10000 -l 1,2,3,6]
127.0.0.1 - - [07/May/2018:17:55:55 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,918 Using dependency bcftools version 1.5 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:55,921 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-05-07 17:55:55,939 (5) command is: rm -rf working; mkdir -p working; cd working; /tmp/tmpva5iYO/job_working_directory/000/5/tool_script.sh; return_code=$?; cd '/tmp/tmpva5iYO/job_working_directory/000/5';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
export PATH=$PATH:'/home/travis/miniconda3/envs/__bcftools@1.5/bin' ; python "/tmp/tmpva5iYO/job_working_directory/000/5/set_metadata__rDIPM.py" "/tmp/tmpva5iYO/job_working_directory/000/5/registry.xml" "/tmp/tmpva5iYO/job_working_directory/000/5/working/galaxy.json" "/tmp/tmpva5iYO/job_working_directory/000/5/metadata_in_HistoryDatasetAssociation_5_z8hYFv,/tmp/tmpva5iYO/job_working_directory/000/5/metadata_kwds_HistoryDatasetAssociation_5_SBFHa8,/tmp/tmpva5iYO/job_working_directory/000/5/metadata_out_HistoryDatasetAssociation_5_JX5o14,/tmp/tmpva5iYO/job_working_directory/000/5/metadata_results_HistoryDatasetAssociation_5_XqQz6d,/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_5.dat,/tmp/tmpva5iYO/job_working_directory/000/5/metadata_override_HistoryDatasetAssociation_5_3Xs3F1" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:55:55,973 (5) executing job script: /tmp/tmpva5iYO/job_working_directory/000/5/galaxy_5.sh
galaxy.jobs DEBUG 2018-05-07 17:55:56,008 (5) Persisting job destination (destination id: planemo_dest)
127.0.0.1 - - [07/May/2018:17:55:56 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:55:56,285 Using dependency bcftools version 1.5 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:55:56,285 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-05-07 17:55:56,294 (6) command is: rm -rf working; mkdir -p working; cd working; /tmp/tmpva5iYO/job_working_directory/000/6/tool_script.sh; return_code=$?; cd '/tmp/tmpva5iYO/job_working_directory/000/6';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
export PATH=$PATH:'/home/travis/miniconda3/envs/__bcftools@1.5/bin' ; python "/tmp/tmpva5iYO/job_working_directory/000/6/set_metadata_7BZP3W.py" "/tmp/tmpva5iYO/job_working_directory/000/6/registry.xml" "/tmp/tmpva5iYO/job_working_directory/000/6/working/galaxy.json" "/tmp/tmpva5iYO/job_working_directory/000/6/metadata_in_HistoryDatasetAssociation_6_v8bSAI,/tmp/tmpva5iYO/job_working_directory/000/6/metadata_kwds_HistoryDatasetAssociation_6_Xv2aww,/tmp/tmpva5iYO/job_working_directory/000/6/metadata_out_HistoryDatasetAssociation_6_LXSWlW,/tmp/tmpva5iYO/job_working_directory/000/6/metadata_results_HistoryDatasetAssociation_6_V84w2z,/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_6.dat,/tmp/tmpva5iYO/job_working_directory/000/6/metadata_override_HistoryDatasetAssociation_6_M5ndOf" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:55:56,324 (6) executing job script: /tmp/tmpva5iYO/job_working_directory/000/6/galaxy_6.sh
galaxy.jobs DEBUG 2018-05-07 17:55:56,342 (6) Persisting job destination (destination id: planemo_dest)
127.0.0.1 - - [07/May/2018:17:55:56 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:56 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:57 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:57 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:57 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:58 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:58 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:58 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:59 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:59 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:59 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:55:59 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:00 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:00 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:00 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:01 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:01 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:01 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:02 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:02 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:02,528 execution finished: /tmp/tmpva5iYO/job_working_directory/000/5/galaxy_5.sh
galaxy.model.metadata DEBUG 2018-05-07 17:56:02,721 loading metadata from file for: HistoryDatasetAssociation 5
127.0.0.1 - - [07/May/2018:17:56:02 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs DEBUG 2018-05-07 17:56:02,967 job 5 ended (finish() executed in (430.035 ms))
127.0.0.1 - - [07/May/2018:17:56:03 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs DEBUG 2018-05-07 17:56:03,315 (7) Working directory for job is: /tmp/tmpva5iYO/job_working_directory/000/7
galaxy.jobs.handler DEBUG 2018-05-07 17:56:03,319 (7) Dispatching to planemo_runner runner
galaxy.jobs DEBUG 2018-05-07 17:56:03,345 (7) Persisting job destination (destination id: planemo_dest)
galaxy.jobs.runners DEBUG 2018-05-07 17:56:03,366 Job [7] queued (31.498 ms)
galaxy.jobs.handler INFO 2018-05-07 17:56:03,373 (7) Job dispatched
127.0.0.1 - - [07/May/2018:17:56:03 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:56:03,537 Using dependency gawk version 4.1.3 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:56:03,538 Using dependency gawk version 4.1.3 of type conda
galaxy.jobs.command_factory INFO 2018-05-07 17:56:03,584 Built script [/tmp/tmpva5iYO/job_working_directory/000/7/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/travis/miniconda3/envs/__gawk@4.1.3" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/travis/miniconda3/bin/activate '/home/travis/miniconda3/envs/__gawk@4.1.3' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; awk --version | head -n 1 > /tmp/tmpva5iYO/tmp/GALAXY_VERSION_STRING_7 2>&1; awk -v OFS=" " --re-interval --sandbox '{ $1 = gensub( /chr20/, "chrX", "g", $1 ) ; print $0 ; }' "/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_5.dat" > "/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_7.dat"]
galaxy.tools.deps DEBUG 2018-05-07 17:56:03,697 Using dependency bcftools version 1.5 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:56:03,700 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-05-07 17:56:03,716 (7) command is: rm -rf working; mkdir -p working; cd working; /tmp/tmpva5iYO/job_working_directory/000/7/tool_script.sh; return_code=$?; cd '/tmp/tmpva5iYO/job_working_directory/000/7';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
export PATH=$PATH:'/home/travis/miniconda3/envs/__bcftools@1.5/bin' ; python "/tmp/tmpva5iYO/job_working_directory/000/7/set_metadata_D3IlAN.py" "/tmp/tmpva5iYO/job_working_directory/000/7/registry.xml" "/tmp/tmpva5iYO/job_working_directory/000/7/working/galaxy.json" "/tmp/tmpva5iYO/job_working_directory/000/7/metadata_in_HistoryDatasetAssociation_7_jRIdWC,/tmp/tmpva5iYO/job_working_directory/000/7/metadata_kwds_HistoryDatasetAssociation_7_xEo8FR,/tmp/tmpva5iYO/job_working_directory/000/7/metadata_out_HistoryDatasetAssociation_7_oJNw0W,/tmp/tmpva5iYO/job_working_directory/000/7/metadata_results_HistoryDatasetAssociation_7_lcfHPq,/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_7.dat,/tmp/tmpva5iYO/job_working_directory/000/7/metadata_override_HistoryDatasetAssociation_7_LNWLcO" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:03,759 (7) executing job script: /tmp/tmpva5iYO/job_working_directory/000/7/galaxy_7.sh
galaxy.jobs DEBUG 2018-05-07 17:56:03,801 (7) Persisting job destination (destination id: planemo_dest)
127.0.0.1 - - [07/May/2018:17:56:03 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:05,901 execution finished: /tmp/tmpva5iYO/job_working_directory/000/6/galaxy_6.sh
galaxy.model.metadata DEBUG 2018-05-07 17:56:06,356 loading metadata from file for: HistoryDatasetAssociation 6
galaxy.jobs DEBUG 2018-05-07 17:56:06,486 job 6 ended (finish() executed in (575.109 ms))
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:09,905 execution finished: /tmp/tmpva5iYO/job_working_directory/000/7/galaxy_7.sh
galaxy.model.metadata DEBUG 2018-05-07 17:56:10,078 loading metadata from file for: HistoryDatasetAssociation 7
127.0.0.1 - - [07/May/2018:17:56:10 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs DEBUG 2018-05-07 17:56:10,218 job 7 ended (finish() executed in (304.016 ms))
127.0.0.1 - - [07/May/2018:17:56:10 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs DEBUG 2018-05-07 17:56:10,516 (8) Working directory for job is: /tmp/tmpva5iYO/job_working_directory/000/8
galaxy.jobs.handler DEBUG 2018-05-07 17:56:10,522 (8) Dispatching to planemo_runner runner
galaxy.jobs DEBUG 2018-05-07 17:56:10,555 (8) Persisting job destination (destination id: planemo_dest)
galaxy.jobs.runners DEBUG 2018-05-07 17:56:10,563 Job [8] queued (41.534 ms)
galaxy.jobs.handler INFO 2018-05-07 17:56:10,589 (8) Job dispatched
galaxy.tools.deps DEBUG 2018-05-07 17:56:10,722 Using dependency gawk version 4.1.3 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:56:10,723 Using dependency gawk version 4.1.3 of type conda
galaxy.jobs.command_factory INFO 2018-05-07 17:56:10,770 Built script [/tmp/tmpva5iYO/job_working_directory/000/8/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/travis/miniconda3/envs/__gawk@4.1.3" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/travis/miniconda3/bin/activate '/home/travis/miniconda3/envs/__gawk@4.1.3' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; awk --version | head -n 1 > /tmp/tmpva5iYO/tmp/GALAXY_VERSION_STRING_8 2>&1; awk -v OFS=" " --re-interval --sandbox '{ $1 = gensub( /chr21/, "chrY", "g", $1 ) ; print $0 ; }' "/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_7.dat" > "/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_8.dat"]
127.0.0.1 - - [07/May/2018:17:56:10 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:56:10,916 Using dependency bcftools version 1.5 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:56:10,916 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-05-07 17:56:10,922 (8) command is: rm -rf working; mkdir -p working; cd working; /tmp/tmpva5iYO/job_working_directory/000/8/tool_script.sh; return_code=$?; cd '/tmp/tmpva5iYO/job_working_directory/000/8';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
export PATH=$PATH:'/home/travis/miniconda3/envs/__bcftools@1.5/bin' ; python "/tmp/tmpva5iYO/job_working_directory/000/8/set_metadata_IFSmTr.py" "/tmp/tmpva5iYO/job_working_directory/000/8/registry.xml" "/tmp/tmpva5iYO/job_working_directory/000/8/working/galaxy.json" "/tmp/tmpva5iYO/job_working_directory/000/8/metadata_in_HistoryDatasetAssociation_8_ucSlHf,/tmp/tmpva5iYO/job_working_directory/000/8/metadata_kwds_HistoryDatasetAssociation_8_WNx57x,/tmp/tmpva5iYO/job_working_directory/000/8/metadata_out_HistoryDatasetAssociation_8_HYBBdx,/tmp/tmpva5iYO/job_working_directory/000/8/metadata_results_HistoryDatasetAssociation_8_2wBZMT,/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_8.dat,/tmp/tmpva5iYO/job_working_directory/000/8/metadata_override_HistoryDatasetAssociation_8_jCfCjK" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:10,943 (8) executing job script: /tmp/tmpva5iYO/job_working_directory/000/8/galaxy_8.sh
galaxy.jobs DEBUG 2018-05-07 17:56:10,962 (8) Persisting job destination (destination id: planemo_dest)
127.0.0.1 - - [07/May/2018:17:56:11 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:11 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:11 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:12 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:12 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:12 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:12 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:13 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:13 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:13 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:14 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:14 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:14 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:15 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:15 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:15 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:15 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:16 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:16,414 execution finished: /tmp/tmpva5iYO/job_working_directory/000/8/galaxy_8.sh
galaxy.model.metadata DEBUG 2018-05-07 17:56:16,583 loading metadata from file for: HistoryDatasetAssociation 8
127.0.0.1 - - [07/May/2018:17:56:16 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs DEBUG 2018-05-07 17:56:16,695 job 8 ended (finish() executed in (272.482 ms))
galaxy.jobs DEBUG 2018-05-07 17:56:16,744 (9) Working directory for job is: /tmp/tmpva5iYO/job_working_directory/000/9
galaxy.jobs.handler DEBUG 2018-05-07 17:56:16,749 (9) Dispatching to planemo_runner runner
galaxy.jobs DEBUG 2018-05-07 17:56:16,784 (9) Persisting job destination (destination id: planemo_dest)
galaxy.jobs.runners DEBUG 2018-05-07 17:56:16,794 Job [9] queued (40.183 ms)
galaxy.jobs.handler INFO 2018-05-07 17:56:16,809 (9) Job dispatched
127.0.0.1 - - [07/May/2018:17:56:16 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:56:17,073 Using dependency bedtools version 2.27.0 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:56:17,074 Using dependency bedtools version 2.27.0 of type conda
galaxy.jobs.command_factory INFO 2018-05-07 17:56:17,113 Built script [/tmp/tmpva5iYO/job_working_directory/000/9/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/travis/miniconda3/envs/__bedtools@2.27.0" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/travis/miniconda3/bin/activate '/home/travis/miniconda3/envs/__bedtools@2.27.0' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; bedtools --version > /tmp/tmpva5iYO/tmp/GALAXY_VERSION_STRING_9 2>&1; bedtools intersect -a '/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_6.dat' -b '/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_8.dat' -wa > '/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_9.dat']
127.0.0.1 - - [07/May/2018:17:56:17 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.tools.deps DEBUG 2018-05-07 17:56:17,359 Using dependency bcftools version 1.5 of type conda
galaxy.tools.deps DEBUG 2018-05-07 17:56:17,360 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-05-07 17:56:17,368 (9) command is: rm -rf working; mkdir -p working; cd working; /tmp/tmpva5iYO/job_working_directory/000/9/tool_script.sh; return_code=$?; cd '/tmp/tmpva5iYO/job_working_directory/000/9';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
export PATH=$PATH:'/home/travis/miniconda3/envs/__bcftools@1.5/bin' ; python "/tmp/tmpva5iYO/job_working_directory/000/9/set_metadata_5EbTCg.py" "/tmp/tmpva5iYO/job_working_directory/000/9/registry.xml" "/tmp/tmpva5iYO/job_working_directory/000/9/working/galaxy.json" "/tmp/tmpva5iYO/job_working_directory/000/9/metadata_in_HistoryDatasetAssociation_9_zZeaER,/tmp/tmpva5iYO/job_working_directory/000/9/metadata_kwds_HistoryDatasetAssociation_9_QrCnCl,/tmp/tmpva5iYO/job_working_directory/000/9/metadata_out_HistoryDatasetAssociation_9_RarP9z,/tmp/tmpva5iYO/job_working_directory/000/9/metadata_results_HistoryDatasetAssociation_9_v3Dx_i,/home/travis/.planemo/profiles/travisworkflowtests/files/000/dataset_9.dat,/tmp/tmpva5iYO/job_working_directory/000/9/metadata_override_HistoryDatasetAssociation_9_UmaJ54" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:17,391 (9) executing job script: /tmp/tmpva5iYO/job_working_directory/000/9/galaxy_9.sh
galaxy.jobs DEBUG 2018-05-07 17:56:17,415 (9) Persisting job destination (destination id: planemo_dest)
127.0.0.1 - - [07/May/2018:17:56:17 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:17 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:18 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:18 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:18 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:19 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:19 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:19 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:20 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:20 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:20 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:21 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:21 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:21 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:21 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:22 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:22 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:22 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:23 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:23 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:23 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:24 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.jobs.runners.local DEBUG 2018-05-07 17:56:24,359 execution finished: /tmp/tmpva5iYO/job_working_directory/000/9/galaxy_9.sh
127.0.0.1 - - [07/May/2018:17:56:24 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
galaxy.model.metadata DEBUG 2018-05-07 17:56:24,560 loading metadata from file for: HistoryDatasetAssociation 9
galaxy.jobs DEBUG 2018-05-07 17:56:24,687 job 9 ended (finish() executed in (315.707 ms))
127.0.0.1 - - [07/May/2018:17:56:24 +0000] "GET /api/histories/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:24 +0000] "GET /api/workflows/5729865256bc2525/invocations/5729865256bc2525?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:24 +0000] "GET /api/histories/5729865256bc2525/contents/b842d972534ccb3e?key=92d25dea635f9d58fad846be9f7870b1 HTTP/1.1" 200 - "-" "python-requests/2.18.4"
127.0.0.1 - - [07/May/2018:17:56:24 +0000] "GET /api/histories/5729865256bc2525/contents/b842d972534ccb3e/display HTTP/1.1" 200 5117103 "-" "python-requests/2.18.4"

Test case [<planemo.runnable.TestCase object at 0x7f2029f19590>] resulted in run response [<planemo.galaxy.activity.GalaxyWorkflowRunResponse object at 0x7f202a1ecd10>]
No file specified for test_output_markdown, skipping test output.
No file specified for test_output_text, skipping test output.
There were problems with 1 test(s) - out of 1 test(s) executed. See /tmp/tmpj9rXrW/tool_test_output.html for detailed breakdown.
wf3-shed-tools.ga_0: failed
Exiting planemo with exit code [1]
]

"The log length has exceeded the limit of 4 MB (this usually means that the test suite is raising the same exception over and over)."

@jmchilton jmchilton force-pushed the shed_workflow_test branch 3 times, most recently from 9dfd6fc to 7f21104 Compare May 8, 2018 12:54
@jmchilton jmchilton force-pushed the shed_workflow_test branch from 7f21104 to 07f407f Compare May 8, 2018 12:55
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jmchilton commented May 9, 2018

This runs too long with no output doing this in nose - even this relatively simple workflow spends too much time installing dependencies and running. The good news is a variant of this actually works standalone with planemo test on Travis. I've started like a template project outlining an potential approach here https://github.com/jmchilton/planemo-workflow-test-template and the build is actually green against a newly published Planemo 0.49.2 and Galaxy 18.01. The approach should work just as well against docker-galaxy-stable once there is an 18.01 version ready to go!

@jmchilton jmchilton closed this May 9, 2018
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@jmchilton